Pipeline for exome and WGS(DF3) pipeline

This pipeline is designed to generate cram files compatible with other studies as discussed in https://doi.org/10.1038/s41467-018-06159-4. The original pipeline is initially written in bash by others. This bash rewrote in snakemake to make it more reproducible and easier to handle. The results are identical when compared in SAM format. After this step, we optimised the pipeline to reduce computational costs.